Muhammad ibn Ali may refer to:

• Muhammad ibn al-Hanafiyyah, (636–700) son of Ali, fourth Imam of Kaysanites Shia
• Muhammad ibn Ali ibn Abdallah, grandson of Abdullah bin Abbas and the father of As-Saffah the first Abbasid Caliph; also Imam of Kaysanites Shia after the death of Abu Hashim
• Muhammad al-Baqir (676–733), son of Ali ibn Husayn (Zayn al-'Ābidin), the fourth Imam according to Mustaali and Nizari Ismaili, the fifth Imam according to Twelvers, Seveners and Karmatians
• Muhammad ibn Ali al-Hadi was the son of Ali al-Hadi and the brother of Hasan al-Askari
• Muhammad ibn `Ali at-Tirmidhi (died {{circa|869}}), Sunni jurist (faqih) and traditionist (muhaddith) of Khorasan, also known as Al-Hakim al-Tirmidhi
• Muhammad ibn Ali ibn al-Layth, Saffarid emir

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